Contacts of the helix formed by residues 282 - 296 (chain L) in PDB entry 1ZUM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 282 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280L ASP 3.9 0.6 + - - -
281L ALA* 1.3 69.5 - - - +
283L MET* 1.3 59.0 + - - +
284L ASP* 3.2 12.5 + - - +
285L TRP* 3.0 35.7 + - + +
286L ALA* 2.8 32.1 + - - +
432L PHE* 5.6 0.8 - - - -
434L LYS* 4.3 27.3 + - + +
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Residues in contact with MET 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277L ILE* 6.2 0.2 - - + -
281L ALA 3.1 8.9 + - - +
282L ASP* 1.3 73.1 + - - +
284L ASP* 1.3 63.7 + - - +
286L ALA* 3.7 3.2 - - - +
287L VAL* 2.9 45.4 + - - +
314L ILE* 3.9 46.0 - - + +
317L GLU* 3.9 24.0 - - + +
318L PHE* 4.0 15.9 - - + +
321L ARG* 3.2 36.3 - - - +
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Residues in contact with ASP 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L ASP* 3.2 8.7 + - - +
283L MET* 1.3 77.7 - - - +
285L TRP* 1.3 62.6 + - - +
287L VAL* 3.5 4.1 + - - +
288L GLU* 3.2 33.2 + - + +
321L ARG* 2.7 30.0 + - - +
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Residues in contact with TRP 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K PHE* 6.4 0.4 - + - -
494K LYS* 3.5 37.5 - - + +
282L ASP* 3.0 26.5 + - + +
284L ASP* 1.3 78.9 - - - +
286L ALA* 1.3 57.1 + - - +
288L GLU* 3.4 16.7 + - - +
289L GLN* 2.9 68.7 + - + +
432L PHE* 3.9 15.5 - + - -
454L ASN* 2.9 30.3 + - + -
455L CYS* 5.3 3.1 - - + -
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Residues in contact with ALA 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ILE* 3.8 32.3 - - + +
281L ALA* 4.4 3.8 - - + -
282L ASP 2.8 23.8 + - - +
283L MET* 3.7 4.7 - - - +
285L TRP* 1.3 73.6 - - - +
287L VAL* 1.3 57.6 + - - +
289L GLN* 4.0 0.5 - - - +
290L ALA* 2.9 31.9 + - - +
318L PHE* 3.9 5.4 - - + -
432L PHE* 3.9 23.2 - - + -
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Residues in contact with VAL 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283L MET* 2.9 44.1 + - - +
284L ASP* 3.8 5.2 - - - +
286L ALA* 1.3 72.8 - - - +
288L GLU* 1.3 68.3 + - + +
290L ALA* 3.3 2.8 + - - +
291L HIS* 3.0 22.5 + - - +
318L PHE* 3.7 19.1 - - + +
321L ARG* 3.9 46.7 - - + +
322L SER* 4.0 11.4 + - - +
325L ARG* 4.7 8.5 - - + -
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Residues in contact with GLU 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284L ASP* 3.2 21.0 + - - +
285L TRP* 3.9 17.7 - - + +
287L VAL* 1.3 77.8 - - + +
289L GLN* 1.3 64.6 + - + +
291L HIS* 3.3 9.3 - - - +
292L PHE* 3.0 27.4 + - - +
325L ARG* 5.0 18.1 + - - +
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Residues in contact with GLN 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L ASN* 4.7 1.1 - - - -
285L TRP* 2.9 69.5 + - + +
286L ALA 4.0 0.4 - - - +
288L GLU* 1.3 78.5 + - - +
290L ALA* 1.3 55.6 + - - +
292L PHE* 3.6 20.6 - - - +
293L ALA* 2.7 37.2 + - - +
432L PHE* 3.4 35.7 - - + -
455L CYS* 4.9 5.6 - - - -
456L TYR* 4.5 10.9 + - + +
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Residues in contact with ALA 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L ASN* 3.6 22.4 + - - +
277L ILE* 4.9 0.9 - - + -
286L ALA 2.9 19.8 + - - +
287L VAL 3.7 2.5 - - - +
289L GLN* 1.3 72.8 - - - +
291L HIS* 1.3 67.0 + - - +
293L ALA* 3.4 2.9 + - - +
294L LEU* 3.2 16.3 + - - +
305L GLY 5.1 0.3 - - - +
308L THR* 4.3 12.4 + - + +
318L PHE* 3.6 25.6 - - + -
322L SER* 5.4 0.4 - - - +
405L MET* 3.5 16.1 - - + +
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Residues in contact with HIS 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287L VAL 3.0 12.5 + - - +
288L GLU 3.3 9.9 - - - +
290L ALA* 1.3 77.2 - - - +
292L PHE* 1.3 60.0 + - + +
294L LEU 3.2 1.6 + - - -
295L PHE* 2.8 66.7 + + - +
322L SER* 5.1 2.1 + - - -
325L ARG* 3.3 70.8 + - + +
326L ALA* 4.1 6.7 + - - -
329L ARG* 3.3 37.3 + - - +
405L MET* 3.8 10.6 - - + +
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Residues in contact with PHE 292 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288L GLU 3.0 17.2 + - - +
289L GLN* 3.7 20.2 - - - +
291L HIS* 1.3 80.7 - - + +
293L ALA* 1.3 67.3 + - - +
294L LEU 3.1 1.2 + - - -
295L PHE* 5.2 0.4 - - - -
296L PHE* 3.1 72.6 + + + +
329L ARG* 6.1 0.9 - - - +
456L TYR* 3.8 11.9 - - + -
457L ASP* 3.7 31.6 - - + -
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Residues in contact with ALA 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L ASN* 4.1 5.8 - - + +
289L GLN 2.7 22.6 + - - +
290L ALA* 3.5 11.9 - - - +
292L PHE* 1.3 74.5 - - - +
294L LEU* 1.3 58.6 + - - +
296L PHE* 5.1 0.9 + - - +
301L CYS* 5.9 0.3 - - - +
304L ALA* 3.5 8.0 - - - +
305L GLY* 2.9 25.2 + - - +
456L TYR* 3.4 44.4 - - + -
457L ASP* 4.3 4.7 - - - +
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Residues in contact with LEU 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290L ALA 3.2 9.4 + - - +
291L HIS 3.2 2.7 + - - +
292L PHE 3.1 0.2 - - - -
293L ALA* 1.3 80.7 - - - +
295L PHE* 1.3 80.8 + - + +
296L PHE 3.4 3.1 + - - +
299L GLY* 3.1 24.6 - - - -
304L ALA* 4.3 7.7 - - + +
305L GLY 3.2 26.5 - - - +
306L SER* 3.4 20.2 - - - -
402L GLY 4.4 2.9 - - - +
403L PRO 4.2 0.2 - - - -
404L VAL 3.3 26.5 - - - +
405L MET* 3.4 44.9 - - + +
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Residues in contact with PHE 295 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291L HIS* 2.8 57.1 + + - +
292L PHE* 5.2 0.2 - - - -
294L LEU* 1.3 83.8 - - + +
296L PHE* 1.3 63.7 + - - +
298L GLN* 3.1 15.8 + - - -
299L GLY* 3.2 4.6 + - - +
322L SER 5.8 0.2 - - - -
326L ALA* 4.3 18.2 - - + -
329L ARG* 3.2 34.2 + - - +
341L GLN* 4.1 6.5 - - - +
383L PRO* 3.9 14.6 - - + -
384L THR 3.9 12.8 - - - -
385L VAL* 4.4 0.4 - - + -
403L PRO* 3.4 39.9 - - + -
405L MET* 3.5 26.2 - - + -
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Residues in contact with PHE 296 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L ILE* 4.1 27.1 - - + -
120L VAL* 4.2 23.6 - - + -
124L MET* 5.6 2.0 - - + -
170L PHE* 3.6 34.5 - + - -
292L PHE* 3.1 58.8 + + + +
293L ALA 5.3 0.7 - - - +
294L LEU 3.4 2.6 - - - +
295L PHE* 1.3 75.0 - - - +
297L ASN* 1.3 76.2 + - + +
299L GLY* 3.0 13.3 + - - -
300L GLN 3.8 1.6 + - - -
301L CYS* 4.5 11.9 - - + +
329L ARG* 4.5 4.0 - - - +
457L ASP* 4.0 20.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il